A graph convolutional network approach for hyperspectral image analysis of blueberries physiological traits under drought stress

• Developed a high-throughput phenotyping platform with hyperspectral imaging. • Introduced Plant-GCN, for estimating physiological traits in blueberries plants. • Plant-GCN achieved high accuracy (R² > 0.90) for predicting physiological traits. • Outperformed traditional statistical and deep learning models. Blueberries are extremely susceptible to drought due to their shallow root systems and limited water regulation capabilities. Climate change exacerbates drought stress in major blueberry production regions, which affect key physiological traits, such as leaf water content (LWC), photosynthesis (A), stomatal conductance (g s ), electron transport rate (ETR), photosystem II efficiency (φPSII) and transpiration rate (E). Current phenotyping methods for measuring these physiological traits are time-consuming and labor-intensive as well as limited by the need for specialized equipment. To address this, a high-throughput phenotyping (HTPP) platform integrated with hyperspectral camera and a novel graph convolutional network (GCN)-based model, Plant-GCN, was developed to predict physiological traits of blueberry plants under drought stress. Spectral reflectance obtained from the hyperspectral images were transformed into a graph representation, with each plant represented as a node, spectral reflectance as node features, and edges defined by spectral similarities. The Plant-GCN model utilizes graph convolutional layers that aggregate information from neighboring nodes, effectively capturing complex interactions in the spectral signature and enhancing the prediction of physiological traits. Plant-GCN achieved a coefficient of determination (R²) of 0.89 for LWC, 0.94 for A, 0.89 for g s , 0.92 for ETR, 0.93 for φPSII and 0.89 for E on the test dataset. The performance of the proposed Plant-GCN model was compared with multilayer perceptron (MLP), partial least squares regression (PLSR), support vector regression (SVR), and random forest (RF), and it consistently outperformed all these models as well as data published in other reports. The high-throughput phenotyping system enabled efficient large-scale data collection, while the Plant-GCN model captured long-range spectral relationships significantly improved the prediction of physiological traits. The high predictability of the models could facilitate the screening of blue-berry cultivars for the specified traits allowing the selection and breeding of new drought tolerant cultivars in the future.